I don't fully understand how ispconfig has postfix configured for looking up addresses from the mysql database. Is there something I can do to make this work? I'm not sure why the aliases table is being disregarded, normally it is always consulted.

I'm using Ubuntu 9.04 Server, fully updated with the most recent ISPConfig 3.

ISPConfig uses the standard virtual user setup as described in the postfix documentation. The aliases file can not be used in a virtual user setup as postfix does not read it for virtual users and domains, the aliases file is only read for setups with linux system users.